MITK Basic Image Processing Mini Apps

Table of Contents

• Description of Mini Apps
  • mitkFileConverter
  • mitkForwardWavelet
  • mitkImageAndValueArithmetic
  • mitkImageTypeCovnerter
  • mitkLaplacianOfGaussian
  • mitkMaskOutlierFiltering
  • mitkMaskRangeBasedFiltering
  • mitkMultiResolutionPyramid
  • mitkResampleImage
  • mitkResampleMask
  • mitkSingleImageArithmetic
  • mitkTwoImageArithmetic

The Basic Image Processing Mini Apps bundle the functionality that is commonly neeeded for the processing of medical images. As all other MiniApps, they follow the Slicer Execution Model in describing themselves via xml. You can simply obtain a description by calling the MiniApp without any parameter. If the MiniApp is calles with the option "--xml" a XML description of all possible parameter is added.

Description of Mini Apps

mitkFileConverter

Allows to convert a file from one type to another file type, for example to convert an image, saved in the nifti format to an image saved in the .nrrd format.

mitkForwardWavelet

Calculates the forward wavelet transformation of an image. The output will consist of multiple images, which will be saved in the format <output>id%<output-extension>, where <output> and <output-extension> are specified by the user and id% is a consecutive number.

mitkImageAndValueArithmetic

Mathematical operations with two operants, the individual voxels of the image and a specified floating point value. By default, the floating point value is the right operand.

mitkImageTypeCovnerter

Convert the data fromat that is used to save a voxel of an image.

mitkLaplacianOfGaussian

Calculate the Laplacian of Gaussian of an image with the specified sigma value.

mitkMaskOutlierFiltering

Can be used to clean an segmentation. The mean and standard deviation of the intensities which are masked is calculated and then all mask voxels are removed that cover image voxels which are not within a 3 sigma range.

mitkMaskRangeBasedFiltering

Removing all voxels from a mask that cover image voxels which are outside of a given range. The range can be either specified by a lower limit, a upper limit, or both at the same time.

mitkMultiResolutionPyramid

Calculate a Multi-Resolution Pyramid of the given image. The resolution is reduced by factor 2 for each step.

mitkResampleImage

Resample a mask to a new spacing

mitkResampleMask

Similar to mitkResampleImage, but specificly tailored to resampling a mask.

mitkSingleImageArithmetic

Applies single operand mathematical operations to each voxel of an image

mitkTwoImageArithmetic

Applied two operand mathematical operations to each voxels of two images.